SHANK2 _LIHC.png
Expression analysis of TCGA samples
Basic Information
VIS ID
TVIS10000476
Fusion event
HBV-SHANK2 integration
Validated
Yes
Detection method
PCR and Sanger sequencing
Data source
Curated
Sample type
Tumor
Disease
Hepatocellular carcinoma (HCC)
Quality evaluation
Perfect
Reported year
2016
PubMed ID
27703150
Virus Sequence
Virus name
HBV
Reference genome
AF090842.1;AB033554.1;AB014381.1;M32138.1;AB032431.1;AB036910.1;AB064310;AY090454.1
Host Sequence
Chromosome
chr11
Cytoband
q13.4
Reference genome
GRCh37/hg19
Start
70791199/70945094 (Hg38)
End
70791199/70945094 (Hg38)
Location type
Intronic
Fragile sites / regions
FRA11H
Target gene
SHANK2
miRNAs that regulate target gene
hsa-mir-1307-3p ; hsa-mir-155-5p ; hsa-mir-4646-3p ; hsa-mir-4433b-5p ; hsa-mir-4433a-5p ; hsa-mir-4469 ; hsa-mir-4667-3p ; hsa-mir-1470 ; hsa-mir-6756-3p ; hsa-mir-3127-3p
Nearest miRNA
hsa-mir-10392/Upstream/72726; hsa-let-7a-2/Downstream/528409;
Nearest TSS
ENST00000527297/Upstream/48527; ENST00000529369/Downstream/5977;
Nearest CpG islands
None/Target, chr11-CpG: 30/Upstream/118144, chr11-CpG: 211/Downstream/306033
Upstream sequence
TGGGAAGTCCGTCTTTTGACAAGAGCCGCCCATACACAATTTCCATCCCCTGCATAAGTGCCTCAAGTAGAAGATGGAGATGGGCAGCTGATAATCA
Target sequence
ACTATTTGTTAATTAACCTTTGAGTTATGAAATTATTGTTGATGCAGCAAATGTGTGGTTGTTTTGGTAGGGACTGTTTAGATTTGTTGAATTTCAGAATCTTAGATGCTT
Junction sequence
TGGGAAGTCCGTCTTTTGACAAGAGCCGCCCATACACAATTTCCATCCCCTGCATAAGTGCCTCAAGTAGAAGATGGAGATGGGCAGCTGATAATCAAACTGTTCTTGAATATTTGGTGTCTTTTGGAGTGTGGATTCGCCCTCCTCCTGC
* Color:  Human Sequence / Virus Sequence / Overlapped sequence / Unknown sequence
Reference
Zhao, L. H., et al.Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma. Nat Commun ,2016,7: 12992.
Curate